Tree Genetics and Molecular Breeding 2024, Vol.14, No.4, 166-176 http://genbreedpublisher.com/index.php/tgmb 168 2.3 Epigenetic modifications influencing stem cell function Epigenetic modifications, including DNA methylation, histone modifications, and non-coding RNA-mediated events, are critical for regulating stem cell function. These modifications establish heritable gene expression patterns that guide stem cell differentiation and maintain cellular memory (Wu and Sun, 2006). Histone acetylation and methylation, for example, play significant roles in promoting or repressing gene expression during cell differentiation (Ikeuchi et al., 2015). The dynamic nature of epigenetic regulation is further exemplified by the role of microRNAs in controlling stem cell fate by repressing the translation of specific mRNAs (Gangaraju and Lin, 2009). The interplay between epigenetic mechanisms and transcriptional networks is essential for maintaining stem cell identity and ensuring proper differentiation (Li and Zhao, 2008; Wutz, 2013). 3 Cellular Level Regulation 3.1 Signaling pathways involved in stem cell regulation Stem cell regulation is critically dependent on various signaling pathways that control their self-renewal, differentiation, and response to environmental cues. Key pathways include the Wnt, Notch, and BMP signaling pathways, which are essential for maintaining stem cell properties and ensuring proper tissue development and regeneration (Zhang and Li, 2005; Guo et al., 2015; Sonnen and Janda, 2021). For instance, the Notch signaling pathway is known to regulate stem cell maintenance and proliferation, and its dysregulation can lead to diseases such as cancer (Figure 2) (Janghorban et al., 2018; Sonnen and Janda, 2021). Similarly, the BMP signaling pathway plays a crucial role in stem cell self-renewal and differentiation across different stem cell systems, including embryonic and hematopoietic stem cells (Zhang and Li, 2005). These pathways often interact with each other and with other cellular mechanisms to create a robust regulatory network that ensures the proper functioning of stem cells. 3.2 Hormonal control and interaction with stem cells Hormones such as auxin and cytokinin are pivotal in regulating stem cell niches, particularly in plant systems. These phytohormones exhibit complex interactions that are crucial for the maintenance and function of stem cells in both shoot and root meristems (Zhao et al., 2010; Schuster et al., 2014; García-Gómez et al., 2017). For example, in the shoot apical meristem (SAM) of Arabidopsis thaliana, cytokinin promotes stem cell proliferation, while auxin has a more nuanced role, sometimes inhibiting cytokinin signaling to fine-tune stem cell activity (Zhao et al., 2010). The interplay between these hormones is mediated by specific transcription factors and response regulators, which integrate hormonal signals to modulate stem cell behavior (Schuster et al., 2014; García-Gómez et al., 2017). This hormonal control is essential for the dynamic regulation of stem cell niches, allowing plants to adapt to environmental changes and developmental cues. 3.3 Cell-to-cell communication and its impact on stem cell behavior Cell-to-cell communication is a fundamental aspect of stem cell regulation, enabling the coordination of stem cell activities within their niches and with surrounding differentiated cells. This communication is mediated through various signaling pathways and direct cell contacts, which collectively influence stem cell fate decisions (Burgess et al., 2014; Guo et al., 2015; Sonnen and Janda, 2021). For instance, signaling pathways such as Wnt and Notch not only regulate stem cell properties but also facilitate interactions between stem cells and their niche, ensuring a balanced environment for stem cell maintenance and differentiation (Guo et al., 2015; Sonnen and Janda, 2021). Additionally, metabolic signals and feedback mechanisms play a significant role in this communication, linking cellular metabolism with stem cell function and ensuring that stem cells can respond appropriately to changes in their microenvironment (Burgess et al., 2014). Understanding these intricate communication networks is crucial for unraveling the complex regulation of stem cells and their roles in development and tissue homeostasis. 4 Tissue and Organ Level Regulation 4.1 Stem cell niches in trees: structure and function Stem cell niches are specialized microenvironments that regulate the behavior of stem cells, ensuring their self-renewal and differentiation. In trees, these niches are crucial for maintaining the balance between stem cell proliferation and differentiation, which is essential for growth and regeneration. The structure of stem cell niches
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